Allele-specific expression analysis
Bioinformatics Platform - Institut Curie
2017-04-24
R –no-save –no-restore -e “outPath=‘./’; inPath=‘/data/kdi_prod/.kdi/project_workspace_0/650/acl/04.00/rna_analysis/results/ascount’; min_gene_cov=‘10’; gene.in=‘/data/kdi_prod/.kdi/project_workspace_0/650/acl/04.00/rna_analysis/annotations/Mus_musculus.NCBIM37.cleaned.gtf’; known.escapees=‘/data/kdi_prod/.kdi/project_workspace_0/650/acl/04.00/rna_analysis/annotations/escapees_Berletch.txt’; rmarkdown::render(‘as_analysis_report.Rmd’, output_file=‘${ODIR}as_analysis_report.html’)”
Mapping statistics
Add stats file with counts
Per sample analysis
Scatter plots of counts per parental genome
B172T12_LXK_L001_R1_val_NCBIM37_Cast_tophat_asratio.tsv
B172T22_LXK_L001_R1_val_NCBIM37_Cast_tophat_asratio.tsv
B189T88_RC6_L001_val_FVB_Cast_NCBIM37_tophat_asratio.tsv
B189T89_RC8_L001_val_FVB_Cast_NCBIM37_tophat_asratio.tsv
B189T90_RC9_L001_val_FVB_Cast_NCBIM37_tophat_asratio.tsv
B99T17_TetMyc_RC3_L001_R1_val_tophat_asratio.tsv
B99T18_TetMyc_RC5_L002_R1_val_tophat_asratio.tsv
B99T19_TetMyc_RC8_L003_R1_val_tophat_asratio.tsv
B99T20_TetMyc_RC9_L004_R1_val_tophat_asratio.tsv
B99T21_TetMyc_RC10_L005_R1_val_tophat_asratio.tsv
B99T22_TetMyc_RC11_L006_R1_val_tophat_asratio.tsv
Boxplots of asratio per chromosome
B172T12_LXK_L001_R1_val_NCBIM37_Cast_tophat_asratio.tsv
B172T22_LXK_L001_R1_val_NCBIM37_Cast_tophat_asratio.tsv
B189T88_RC6_L001_val_FVB_Cast_NCBIM37_tophat_asratio.tsv
B189T89_RC8_L001_val_FVB_Cast_NCBIM37_tophat_asratio.tsv
B189T90_RC9_L001_val_FVB_Cast_NCBIM37_tophat_asratio.tsv
B99T17_TetMyc_RC3_L001_R1_val_tophat_asratio.tsv
B99T18_TetMyc_RC5_L002_R1_val_tophat_asratio.tsv
B99T19_TetMyc_RC8_L003_R1_val_tophat_asratio.tsv
B99T20_TetMyc_RC9_L004_R1_val_tophat_asratio.tsv
B99T21_TetMyc_RC10_L005_R1_val_tophat_asratio.tsv
B99T22_TetMyc_RC11_L006_R1_val_tophat_asratio.tsv
Heatmaps
X chromosome
Known escapees
Escapees
